![]() ![]() The power of NGS might thus be of particular interest in that cases for reconstructing full genomes of pathogens directly from nucleic acids extracted from clinical samples. Such information, that could only be retrieved from whole genome sequencing (WGS), usually requires culture of the pathogen, which can be unsuccessful in the majority of cases (and particularly for viruses and other intracellular organisms which need host cells), can take several weeks for fastidious microorganisms or can be prevented by early administration of antimicrobial drugs. In addition, PCR will provide only partial information on the genetic diversity, genotype, functional potential, nutritional requirements as well as virulence or antibiotic-resistance. However, and precisely because of its high specificity, PCR may not detect microorganisms whose sequences are too divergent from those targeted by the primers and probes designed. PCR has numerous advantages, such as low cost, rapid processing and results acquisition, automation, sensitivity and specificity. This approach, which is based on the amplification of a generally short and conserved genomic region, can provide information on the presence/absence and abundance of a targeted microbial pathogen. So far, polymerase chain reaction (PCR) has been the gold standard method for the clinical diagnosis of infectious diseases ( Edwards and Gibbs, 1994). This issue is particularly problematic in the field of infectious disease diagnostic, where the rapid identification and functional characterization of a particular pathogen is critical for the clinical management of infected patients. Unbiased ultra-deep sequencing of complex samples is now accessible, although bioinformatics analyses may still be long and tedious. The development of next-generation sequencing (NGS) approaches has revolutionized human clinical research because of its ability to rapidly generate large volumes of sequencing data per run, with a concomitant decrease of sequencing costs ( Shendure and Ji, 2008).
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